This was only the second time the two nations have met at the finals, with the East Africans emerging victorious in a semi-final clash in 1978.
Uganda knew they needed a similar result in Fes, with only a win enough to send them into the second round.
And while Chelle had the luxury of resting players such as Alex Iwobi, Wilfred Ndidi and Ademola Lookman after the 3-2 win against Tunisia, Cranes boss Paul Put gave starts to St Johnstone striker Uche Ikpeazu, who scored his side’s equaliser against Tanzania and has a Nigerian father, and winger Denis Omedi.
Trabzonspor frontman Onuachu redeemed himself in breaking the deadlock, having squandered a golden opportunity shortly beforehand when Onyango made a smothering point-blank save.
But the Mamelodi Sundowns stopper, who came out of international retirement for this tournament, was soon down again for the wrong reason, receiving treatment after appearing to twist his ankle on the uneven surface underneath a groundsheet displaying a sponsor’s logo behind his goal.
After going down twice more before the break, it was no surprise to see Onyango replaced as part of a triple change by Put ahead of the second half.
The Belgian coach’s plans were soon in disarray after Magoola’s red card and from that point on Uganda never looked capable of a comeback.
A second Nigeria goal felt inevitable and arrived when Fulham’s Samuel Chukwueze released Onyedika down the right, slotting a low finish through Alionzi’s legs to sum up Uganda’s goalkeeping nightmare.
The Club Brugge midfielder netted again in the 67th minute following another incisive attack orchestrated by the lively Chukwueze.
Despite the convincing scoreline, Chelle will be disappointed by the late lapse in concentration which allowed Mato to score the Cranes’ consolation and deny Nigeria a first clean sheet of the tournament.
The victory, however, sees the Super Eagles become the first team to win all three group matches at this Afcon and exhibited the squad’s strength in depth.
For Uganda – and, in particular, the legendary Onyango – this was a sad way to bow out.
